The effects of fuel composition on emissions levels from compression ignition engines can be profound, and this understanding has led to mandated reductions in both sulfur and aromatic content of automotive diesel fuels. A Navistar T444E (V8, 7.3 liter) engine was installed on an engine dynamometer and subjected to transient emissions measurement using a variety of fuels, namely federal low sulfur pump diesel; California pump diesel; Malaysian Fischer-Tropsch fuel with very low sulfur and aromatic content; various blends of soy-derived biodiesel; a Fischer-Tropsch fuel with very low sulfur and 10% aromatics; and the same Fischer-Tropsch fuel with 10% isobutanol by volume. The biodiesel blends showed their ability to reduce particulate matter, but at the expense of increasing oxides of nitrogen (NOx), following the simple argument that cetane enhancement led to earlier ignition. However, the Fischer-Tropsch fuels showed their ability to reduce all of the regulated emissions. In particular, the fuel with ultra low sulfur and aromatic content showed a noticeable benefit over present day California fuel. Adding the alcohol isobutanol to the Fischer-Tropsch diesel reduced oxides of nitrogen and particulate matter over the straight Fischer-Tropsch fuel, but hydrocarbon levels were raised to the extent that the (NOx plus hydrocarbons) level rose. In several of the runs, continuous particulate matter emission levels were measured using a tapered element oscillating microbalance (TEOM), thereby providing deeper insight into the emissions behavior of the fuels.